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Host-specific asymmetric accumulation of mutation types reveals that the origin of SARS-CoV-2 is consistent with a natural process

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The Innovation 2021年第4期2卷 43-55页

作者： ke-jia shan Changshuo Wei Yu Wang Qing Huan Wenfeng Qian State key Laboratory of Plant Genomics Institute of Genetics and Developmental BiologyInnovation Academy for Seed DesignChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China

The capacity of RNA viruses to adapt to new hosts and rapidly escape the host immune system is largely attributable to de novo genetic diversity that emerges through mutations in *** the molecular spectrum of de novo mutations—the relative rates at which various base substitutions occur—are widely recognized as informative toward understanding the evolution of a viral genome,little attention has been paid to the possibility of using molecular spectra to infer the host origins of a ***,we characterize the molecular spectrum of de novo mutations for SARS-CoV-2 from transcriptomic data obtained from virus-infected cell lines,enabled by the use of sporadic junctions formed during discontinuous transcription as molecular *** find that de novo mutations are generated in a replication-independent manner,typically on the genomic strand,and highly dependent on mutagenic mechanisms specific to the host cellular *** novo mutations will then strongly influence the types of base substitutions accumulated during SARS-CoV-2 evolution,in an asymmetric manner favoring specific mutation ***,similarities between the mutation spectra of SARS-CoV-2 and the bat coronavirus RaTG13,which have accumulated since their divergence strongly suggest that SARS-CoV-2 evolved in a host cellular environment highly similar to that of bats before its zoonotic transfer into ***,our findings provide data-driven support for the natural origin of SARS-CoV-2.

关键词： SARS-CoV-2 molecular spectrum de novo mutations mutational signature evolutionary origin mRNA mutation

Molecular Evolution of Protein Sequences and Codon Usage in Monkeypox Viruses

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Genomics, Proteomics & Bioinformatics 2024年第1期22卷 89-97页

作者： ke-jia shan Changcheng Wu Xiaolu Tang Roujian Lu Yaling Hu Wenjie Tan jian Lu State key Laboratory of Protein and Plant Gene Research Center for BioinformaticsSchool of Life SciencesPeking UniversityBeijing 100871China Sinovac Biotech Ltd. Beijing 100085China NHC key Laboratory of Biosafety National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijing 100052China

The monkeypox virus(mpox virus,MPXV)epidemic in 2022 has posed a significant public health ***,the evolutionary principles of MPXV remain largely ***,we examined the evolutionary patterns of protein sequences and codon usage in *** first demonstrated the signal of positive selection in OPG027,specifically in the CladeⅠlineage of ***,we discovered accelerated protein sequence evolution over time in the variants responsible for the 2022 ***,we showed strong epistasis between amino acid substitutions located in different *** codon adaptation index(CAI)analysis revealed that MPXV genes tended to use more non-preferred codons compared to human genes,and the CAI decreased over time and diverged between clades,with CladeⅠ>Ⅱa andⅡb-A>Ⅱ*** the decrease in fatality rate among the three groups aligned with the CAI pattern,it remains unclear whether this correlation was coincidental or if the deoptimization of codon usage in MPXV led to a reduction in fatality *** study sheds new light on the mechanisms that govern the evolution of MPXV in human populations.

关键词： Mpox virus Positive selection OPG027 Accelerated evolution Codon usage bias

Rapid identification of full-length genome and tracing variations of monkeypox virus in clinical specimens based on mNGS and amplicon sequencing

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Virologica Sinica 2024年第1期39卷 134-143页

作者： Changcheng Wu Ruhan A Sheng Ye Fei Ye Weibang Huo Roujian Lu Yue Tang jianwei Yang Xuehong Meng Yun Tang Shuang Chen Li Zhao Baoying Huang Zhongxian Zhang Yuda Chen Dongfang Li Wenling Wang ke-jia shan jian Lu Wenjie Tan NHC key Laboratory of Biosafety National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijing100052China Chongqing Municipal key Laboratory for High Pathogenic Microbes Chongqing Center for Disease Control and PreventionChongqing400042China MGI BGI-ShenzhenShenzhen518083China Thermo Fisher Scientific Beijing100013China School of Public Health Baotou Medical CollegeBaotou014030China BGI PathoGenesis Pharmaceutical Technology Shenzhen518000China State key Laboratory of Protein and Plant Gene Research Center for BioinformaticsSchool of Life SciencesPeking UniversityBeijing100871China College of Life Sciences University of Chinese Academy of SciencesBeijing100049China

The monkeypox virus(MPXV)has triggered a current outbreak *** sequencing of MPXV and rapid tracing of genetic variants will benefit disease diagnosis and *** is a significant challenge but necessary to optimize the strategy and application of rapid full-length genome identification and to track variations of MPXV in clinical specimens with low viral loads,as it is one of the DNA viruses with the largest genome and the most AT-biased,and has a significant number of tandem *** we evaluated the performance of metagenomic and amplicon sequencing techniques,and three sequencing platforms in MPXV genome sequencing based on multiple clinical specimens of five mpox cases in Chinese *** rapidly identified the full-length genome of MPXV with the assembly of accurate tandem repeats in multiple clinical *** sequencing enables cost-effective and rapid sequencing of clinical specimens to obtain high-quality MPXV ***-generation sequencing facilitates the assembly of the terminal tandem repeat regions in the monkeypox virus genome and corrects a common misassembly in published ***,several intra-host single nucleotide variations were identified in the first imported mpox *** study offers an evaluation of various strategies aimed at identifying the complete genome of MPXV in clinical *** findings of this study will significantly enhance the surveillance of MPXV.

关键词： Monkeypox virus(MPXV) Metagenomic Next generation sequencing Amplicon Third-generation sequencing

大型桥梁勘测设计的质量问题分析和质量监控体系

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工程与建设 2024年第1期38卷 60-62页

作者：贾科善黔南州交通设计院有限责任公司贵州都匀558000

本文围绕大型桥梁勘测设计的质量问题展开深入分析,强调了地质勘测、设计方案、施工图设计、环境影响评估以及监测与维护等关键环节可能存在的质量风险。通过对质量监控体系的建设提出了具体的方法和技术,包括质量管理体系的建立、质量... 详细信息

本文围绕大型桥梁勘测设计的质量问题展开深入分析,强调了地质勘测、设计方案、施工图设计、环境影响评估以及监测与维护等关键环节可能存在的质量风险。通过对质量监控体系的建设提出了具体的方法和技术,包括质量管理体系的建立、质量监控方法和技术的应用、质量检测与评价以及质量改进与持续优化的机制。最后,强调了质量信息化管理在大型桥梁勘测设计中的关键作用,包括信息收集和整理、分析和报告,以及信息共享和交流。

关键词：大型桥梁勘测设计质量问题监控体系信息化管理

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军事软毁伤效应综合评估与决策分析

火力与指挥控制 2005年第4期30卷 38-40页

作者：柯加山程刚吉利强军事科学院军事运筹分析研究所北京100091 炮兵学院安徽合肥230031 军械工程学院河北石家庄050003

军事打击不但可以直接毁伤敌方政治、军事目标,而且可以造成敌方社会秩序混乱、经济发展受挫、人民心理恐慌等军事软毁伤效应。军事软毁伤效应在未来信息化战争中很有可能达成显著的战略目标,因此,研究军事软毁伤效应具有重要而现实的... 详细信息

军事打击不但可以直接毁伤敌方政治、军事目标,而且可以造成敌方社会秩序混乱、经济发展受挫、人民心理恐慌等军事软毁伤效应。军事软毁伤效应在未来信息化战争中很有可能达成显著的战略目标,因此,研究军事软毁伤效应具有重要而现实的意义。依据软毁伤理论,建立了军事软毁伤效应的综合评估指标体系,给出了一种军事软毁伤效应的综合评估模型,并设计了综合评估决策支持系统。

关键词：军事软毁伤指标体系综合评估决策支持系统

Predictive value of a constructed artificial neural network model for microvascular invasion in hepatocellular carcinoma:A retrospective study

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World Journal of Gastrointestinal Oncology 2025年第1期17卷 88-100页

作者： Hai-Yang Nong Yong-Yi Cen shan-Jin Lu Rui-Sui Huang Qiong Chen Li-Feng Huang jian-Ning Huang Xue Wei Man-Rong Liu Lin Li ke Ding Department of Radiology The Third Affiliated Hospital of Guangxi Medical UniversityNanning 530031Guangxi Zhuang Autonomous RegionChina Department of Radiology Affiliated Hospital of Youjiang Medical University for NationalitiesBaise 533000Guangxi Zhuang Autonomous RegionChina Guangxi Clinical Medical Research Center for Hepatobiliary Diseases Affiliated Hospital of Youiiang Medical University for NationalitiesBaise 533000Guangxi Zhuang Autonomous RegionChina Department of Ultrasound The Third Affiliated Hospital of Guangxi Medical UniversityNanning 530031Guangxi Zhuang Autonomous RegionChina Department of Hepatobiliary Surgery The Third Affiliated Hospital of Guangxi Medical UniversityNanning 530031Guangxi Zhuang Autonomous RegionChina

BACKGROUND Microvascular invasion(MVI)is a significant risk factor for recurrence and metastasis following hepatocellular carcinoma(HCC)***,there is a paucity of preoperative evaluation approaches for *** To investigate the predictive value of texture features and radiological signs based on multiparametric magnetic resonance imaging in the non-invasive preoperative prediction of MVI in *** Clinical data from 97 HCC patients were retrospectively collected from January 2019 to July 2022 at our *** were classified into two groups:MVI-positive(n=57)and MVI-negative(n=40),based on postoperative pathological *** correlation between relevant radiological signs and MVI status was ***4.6 software and the mutual information method were employed to identify the top 10 dominant texture features,which were combined with radiological signs to construct artificial neural network(ANN)models for MVI *** predictive performance of the ANN models was evaluated using area under the curve,sensitivity,and *** models with relatively high predictive performance were screened using the DeLong test,and the regression model of multilayer feedforward ANN with backpropagation and error backpropagation learning method was used to evaluate the models’*** The absence of a pseudocapsule,an incomplete pseudocapsule,and the presence of tumor blood vessels were identified as independent predictors of HCC *** ANN model constructed using the dominant features of the combined group(pseudocapsule status+tumor blood vessels+arterial phase+venous phase)demonstrated the best predictive performance for MVI status and was found to be automated,highly operable,and very *** The ANN model constructed using the dominant features of the combined group can be recommended as a noninvasive method for preoperative prediction of HCC MVI status.

关键词： Hepatocellular carcinoma Texture analysis Magnetic resonance imaging Microvascular invasion Pseudocapsule Tumor blood vessels

Primary parenchymal squamous cell carcinoma of the kidney:A case report

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World Journal of Clinical Cases 2025年第4期13卷 34-40页

作者： Zhi-Hui Zheng Bo Shao Chao-Min Xu ke Wang jia-Zhu Wen Li-Kang Luo jia-Cheng Guan Department of Ultrasound The Second People’s Hospital of QuzhouQuzhou 324000Zhejiang ProvinceChina Department of Radiology Shulan(Quzhou)HospitalQuzhou 324000Zhejiang ProvinceChina Department of Radiology The Second People’s Hospital of QuzhouQuzhou 324000Zhejiang ProvinceChina Department of Pathology The Second people’s Hospital of QuzhouQuzhou 324000Zhejiang ProvinceChina

BACKGROUND Primary squamous cell carcinoma(SCC)of the renal parenchyma is extremely rare,with only nine cases *** SUMMARY This study reports a 51-year-old man with primary SCC of the renal *** patient was admitted with recurrent dull pain and discomfort in the right lumbar region,which had worsened over 2 weeks,accompanied by painful gross *** antigen(SCCA)levels were elevated,and imaging revealed a renal mass with associated *** patient underwent laparoscopic unilateral nephrectomy and lymph node *** pathology confirmed highly differentiated SCC with necrosis in the right renal parenchyma,with negative renal pelvis and *** pathological stage was *** months after surgery,the tumor recurred with involvement of the liver,right psoas major muscle,and inferior vena *** patient refused chemotherapy and succumbed to the disease 6 months postoperatively due to disease *** We report a case of primary SCC of the renal parenchyma,a rare renal *** clinical symptoms,laboratory tests,and imaging findings are nonspecific,making accurate and timely diagnosis *** to the literature,for patients with renal calculi accompanied by a renal mass,elevated serum SCCA levels,and magnetic resonance imaging showing cystic or cystic-solid masses within the kidney with pseudocapsules and heterogeneous mild enhancement,the possibility of this disease should be considered.

关键词： Renal tumor Renal parenchyma Squamous cell carcinoma Renal calculi Computed tomography Case report

Prediction and stratification for the surgical adverse events after minimally invasive esophagectomy:A two-center retrospective study

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World Journal of Gastroenterology 2025年第3期31卷 50-61页

作者： Qi-Hong Zhong jiang-shan Huang Fei-Long Guo Jing-Yu Wu Mao-Xiu Yuan jia-Fu Zhu Wen-Wei Lin Sui Chen Zhen-Yang Zhang jiang-Bo Lin Department of Thoracic Surgery Fujian Medical University Union HospitalFuzhou 350001Fujian ProvinceChina The Graduate School Fujian Medical UniversityFuzhou 350001Fujian ProvinceChina Department of Thoracic Surgery Affiliated Hospital of Jinggangshan UniversityJi’an 343000Jiangxi ProvinceChina

BACKGROUND Minimally invasive esophagectomy(MIE)is a widely accepted treatment for esophageal cancer,yet it is associated with a significant risk of surgical adverse events(SAEs),which can compromise patient recovery and long-term *** preoperative identification of high-risk patients is critical for improving *** To establish and validate a risk prediction and stratification model for the risk of SAEs in patients with *** This retrospective study included 747 patients who underwent MIE at two centers from January 2019 to February *** were separated into a train set(n=549)and a validation set(n=198).After screening by least absolute shrinkage and selection operator regression,multivariate logistic regression analyzed clinical and intraoperative variables to identify independent risk factors for SAEs.A risk stratification model was constructed and validated to predict the probability of *** SAEs occurred in 10.2%of patients in train set and 13.6%in the validation *** with SAE had significantly higher complication rate and a longer hospital stay after *** key independent risk factors identified included chronic obstructive pulmonary disease,a history of alcohol consumption,low forced expiratory volume in the first second,and low albumin *** stratification model has excellent prediction accuracy,with an area under the curve of 0.889 for the training set and an area under the curve of 0.793 for the validation *** The developed risk stratification model effectively predicts the risk of SAEs in patients undergoing MIE,facilitating targeted preoperative interventions and improving perioperative management.

关键词： Surgical adverse events Minimally invasive esophagectomy Esophageal cancer Stratification model Perioperative management

Large Time Behavior of Solutions to a 3D keller-Segel-Stokes System Involving a Tensor-valued Sensitivity with Saturation

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Acta Mathematicae Applicatae Sinica 2023年第4期39卷 1032-1064页

作者： Yuan-yuan ke jia-shan ZHENG School of Mathematics Renmin University of ChinaBeijing 100872China School of Mathematics and Statistics Science Yantai UniversityYantai 264005China

In this paper we deal with the initial-boundary value problem for the coupled keller-Segel-Stokes system with rotational flux, which is corresponding to the case that the chemical is produced instead of consumed,■subject to the boundary conditions( n-n S(x, n, c) c) · ν = c · ν = 0 and u = 0, and suitably regular initial data(n0(x), c0(x), u0(x)), where ? ? R3is a bounded domain with smooth boundary ??. Here S is a chemotactic sensitivity satisfying |S(x, n, c)| ≤ CS(1 + n)-αwith some CS> 0 and α > 0. The greatest contribution of this paper is to consider the large time behavior of solutions for the system(KSS), which is still open even in the 2D case. We can prove that the corresponding solution of the system(KSS) decays to(■) exponentially, if the coefficient of chemotactic sensitivity is appropriately small. As a precondition to consider the asymptotic behavior, we also show the global existence and boundedness of the corresponding initial-boundary problem KSS with a simplified method. We find a new phenomenon that the suitably small coefficient CSof chemotactic sensitivity could benefit the global existence and boundedness of solutions to the model KSS.

关键词： Large time behavior Global existence Boundedness keller-Segel-Stokes system